Contacts of the helix formed by residues 340 - 359 (chain A) in PDB entry 1EBF
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 340 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA* 1.3 78.8 - - - +
341A ALA* 1.3 66.3 - - - -
342A ALA 3.5 2.2 + - - -
343A VAL* 3.5 4.2 + - - -
344A THR* 2.8 27.6 + - - -
2109A NAD 3.5 13.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.7 37.5 - - + +
16A VAL* 4.7 11.0 - - - -
19A ALA* 4.0 9.5 - - + +
340A GLY* 1.3 69.7 - - - +
342A ALA* 1.3 59.5 + - - +
344A THR* 4.0 0.9 - - - -
345A ALA* 3.0 32.2 + - - +
2109A NAD 5.0 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ALA* 4.4 5.3 - - + +
23A GLN* 3.0 31.7 + - - +
340A GLY 3.6 0.2 - - - -
341A ALA* 1.3 78.4 - - - +
343A VAL* 1.3 59.1 + - + +
346A ALA* 3.1 17.8 + - - +
327B ARG* 4.1 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA* 4.3 7.0 - - + -
149A GLY* 3.7 17.5 - - - +
337A ALA* 4.4 12.3 - - + +
339A ALA 4.6 7.2 - - - +
340A GLY 3.5 6.5 + - - +
341A ALA 3.4 0.2 - - - -
342A ALA* 1.3 78.6 - - + +
344A THR* 1.3 62.3 + - - +
346A ALA* 3.5 6.3 + - - +
347A GLY 3.3 14.9 + - - -
327B ARG* 3.8 34.1 - - + +
328B TYR* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 4.1 20.9 - - + -
115A PRO* 4.5 3.1 - - + -
144A ALA* 4.0 18.1 - - + +
148A ALA* 3.5 22.5 - - - +
149A GLY 4.4 1.3 - - - +
339A ALA 3.9 0.2 - - - -
340A GLY 2.8 30.3 + - - -
341A ALA 4.0 1.8 - - - -
343A VAL* 1.3 73.5 - - - +
345A ALA* 1.3 66.6 + - - +
347A GLY* 3.2 10.4 + - - -
348A VAL* 3.2 13.3 + - - +
2109A NAD 3.8 29.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 3.7 17.2 - - + +
19A ALA 4.0 0.7 - - - -
20A PHE* 3.5 39.4 - - + +
23A GLN* 3.7 11.2 - - - +
341A ALA 3.0 18.2 + - - +
344A THR* 1.3 77.5 - - - +
346A ALA* 1.3 57.1 + - - +
348A VAL* 3.3 7.5 + - - +
349A LEU* 2.8 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 3.1 8.7 + - - +
342A ALA 3.1 19.1 + - - +
343A VAL* 3.7 7.9 - - - +
344A THR 3.2 0.2 - - - -
345A ALA* 1.3 76.9 - - - +
347A GLY* 1.3 55.3 + - - +
349A LEU* 3.6 1.3 - - - +
350A GLY* 2.7 30.7 + - - -
158B GLU* 4.2 3.8 - - - +
159B ILE* 5.7 7.0 - - + -
162B THR* 3.1 29.9 + - + -
327B ARG* 3.4 11.9 - - - +
328B TYR* 6.1 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLU* 4.2 10.0 - - - +
144A ALA* 4.8 4.3 - - - -
148A ALA 4.7 2.9 - - - -
149A GLY* 3.9 22.4 - - - -
343A VAL 3.3 5.5 + - - -
344A THR 3.2 7.9 + - - -
346A ALA* 1.3 76.2 - - - +
348A VAL* 1.3 65.1 + - - +
350A GLY* 3.4 1.6 + - - -
351A ASP* 3.0 25.3 + - - +
158B GLU* 4.6 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A VAL* 5.1 1.3 - - + -
20A PHE* 3.9 8.3 - - + -
90A VAL* 3.8 29.4 - - + -
92A ASN* 3.9 9.9 - - - +
113A ALA* 4.2 17.9 - - + +
114A THR* 4.3 2.0 - - - +
115A PRO* 3.9 20.4 - - + -
144A ALA* 3.6 19.3 - - + -
344A THR* 3.2 17.2 + - + +
345A ALA* 3.6 8.3 - - - +
346A ALA 3.2 0.4 - - - -
347A GLY* 1.3 72.8 - - - +
349A LEU* 1.3 66.9 + - - +
351A ASP* 2.9 18.2 + - - +
352A VAL* 2.9 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 349 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PHE* 3.8 18.3 - - + +
23A GLN* 3.6 39.5 - - + +
24A LEU* 4.0 13.0 - - + +
27A MET* 3.2 39.9 - - + -
345A ALA 2.8 17.6 + - - +
346A ALA* 3.6 6.7 - - - +
348A VAL* 1.3 77.2 - - - +
350A GLY* 1.3 63.5 + - - +
352A VAL* 2.9 30.7 + - + +
353A ILE* 2.9 12.7 + - + +
162B THR* 3.8 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ALA 2.7 20.7 + - - -
347A GLY 3.4 1.3 + - - -
348A VAL 3.2 0.2 - - - -
349A LEU* 1.3 73.2 - - - +
351A ASP* 1.3 56.7 + - - +
353A ILE* 3.3 12.3 + - - +
354A LYS* 3.1 30.4 + - - +
158B GLU* 3.6 34.5 - - - +
162B THR* 4.3 1.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ALA* 4.2 9.6 - - + -
114A THR 5.0 1.6 + - - +
141A TYR* 3.2 33.7 - - + +
142A HIS* 3.7 0.2 - - - -
143A GLU* 2.8 46.4 + - - +
144A ALA 4.6 0.7 + - - -
347A GLY 3.0 7.6 + - - +
348A VAL* 2.9 15.4 + - - +
350A GLY* 1.3 75.2 - - - +
352A VAL* 1.3 62.3 + - - +
354A LYS* 3.2 24.7 + - - +
355A ILE* 3.1 28.7 + - - +
158B GLU* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.8 9.2 - - + -
20A PHE* 4.0 16.4 - - + -
24A LEU* 5.7 1.3 - - + -
33A TYR* 3.7 26.2 - - + -
88A ILE* 4.0 14.0 - - + +
90A VAL* 3.9 19.3 - - + -
113A ALA* 3.7 19.5 - - + -
348A VAL 2.9 16.9 + - - +
349A LEU* 2.9 18.6 + - + +
351A ASP* 1.3 76.3 - - - +
353A ILE* 1.3 57.4 + - - +
355A ILE* 3.3 6.7 + - - +
356A ALA* 2.9 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET* 3.1 38.6 - - + -
33A TYR* 3.7 20.2 - - + +
349A LEU* 2.9 18.2 + - + +
350A GLY* 3.5 14.8 - - - +
351A ASP 3.2 0.2 - - - -
352A VAL* 1.3 75.8 - - - +
354A LYS* 1.3 64.2 + - + +
356A ALA* 3.8 0.5 - - - +
357A GLN* 2.9 49.4 + - - +
158B GLU* 4.7 3.8 - - + +
161B GLN* 3.8 42.6 - - + +
162B THR* 4.6 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.8 29.0 + - + +
143A GLU* 4.9 2.2 + - - -
154A SER* 4.5 23.0 + - - -
350A GLY 3.1 12.7 + - - +
351A ASP* 3.2 29.8 + - - +
353A ILE* 1.3 76.7 - - + +
355A ILE* 1.3 62.2 + - - +
357A GLN* 3.8 8.5 + - - +
358A ARG* 3.4 20.4 + - - +
158B GLU* 2.7 32.7 + - - +
354B LYS* 6.3 2.9 - - - -
357B GLN* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ILE* 3.6 26.2 - - + -
111A SER* 3.6 24.2 - - - +
112A ILE 3.5 32.3 - - - +
113A ALA* 4.1 6.3 - - + -
139A PHE* 4.0 11.7 - - + +
141A TYR* 3.5 28.9 - - + -
351A ASP 3.1 16.7 + - - +
352A VAL 3.8 3.4 - - - +
353A ILE 3.2 0.2 - - - -
354A LYS* 1.3 76.1 - - - +
356A ALA* 1.3 65.2 + - - +
358A ARG* 3.0 16.4 + - - +
359A LEU* 3.0 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER 2.9 20.6 - - - +
6A VAL* 4.2 20.1 - - + +
31A ILE* 3.9 6.6 - - + +
33A TYR* 3.1 40.4 - - + +
88A ILE* 3.9 7.6 - - + +
352A VAL 2.9 14.6 + - - +
353A ILE 3.8 1.8 - - - +
355A ILE* 1.3 78.8 - - - +
357A GLN* 1.3 58.4 + - - +
359A LEU* 3.6 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 2.9 26.1 + - - +
31A ILE* 4.2 13.6 - - + +
353A ILE* 2.9 37.2 + - + +
354A LYS* 4.3 7.2 - - - +
355A ILE 3.2 0.6 - - - -
356A ALA* 1.3 76.7 - - - +
358A ARG* 1.3 62.3 + - - +
359A LEU 3.3 0.2 - - - -
141B TYR* 4.1 4.7 + - - -
161B GLN* 4.7 7.5 + - - +
357B GLN 3.4 1.4 - - - +
358B ARG* 3.2 70.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 5.1 0.6 - - - -
133A ASN* 3.6 15.6 + - - -
139A PHE* 3.2 56.6 - - + +
141A TYR* 2.8 33.6 + - - -
354A LYS 3.4 11.9 + - - +
355A ILE* 3.0 11.5 + - - +
357A GLN* 1.3 80.0 - - - +
359A LEU* 1.3 59.9 + - - +
4B LYS* 4.9 3.8 + - - -
30B THR* 4.6 9.3 + - - -
31B ILE* 5.8 3.6 - - - +
357B GLN* 3.2 60.6 - - + +
359B LEU* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.1 32.5 + - - +
3A THR* 2.9 28.5 + - - +
6A VAL* 4.7 5.4 - - + -
86A PRO* 3.3 40.8 - - + +
87A VAL 4.6 1.8 - - - +
88A ILE* 3.9 19.7 - - + -
109A GLY 6.0 2.0 - - - +
111A SER* 4.0 9.9 - - - +
138A GLY* 6.0 0.9 - - - -
139A PHE* 3.8 27.4 - - + -
355A ILE* 3.0 33.6 + - + +
356A ALA 3.6 4.7 + - - +
357A GLN 3.3 0.4 - - - -
358A ARG* 1.3 79.4 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il